There is known a technique in which, in a fuel cell system including two fuel cell stacks of a start-up stack and a main stack, start-up is performed by using only the start-up stack and exhaust of the start-up stack is supplied to the main stack to heat the main stack in short time (see Patent Literature 1). The start-up stack is connected to a start-up load during the start-up and is shut down, switched to a standby status, or connected to the main stack when the heating of the main stack is completed.